I've done two migrations from old computers to new ones in the past week, and both ended up with permission issues after the process was done. What happened was that nothing seemed to work properly afterwards and the computers would be stuck in an endless loop with an error message saying "macOS needs to repair your library," like:
Typing in password (or using touch ID) to allow the "repair" to not work well and each computer was quite useless with constant alert pop ups. When I checked the permissions on a machine, I found that the user's folders desktop, documents and so on were owned by root . If you know something about the macros underground, then … well … you know it's just bad. I do not remember the last time I had such an "oh holy villain" moment in my stomach.
If you get this issue, Apple has a support article about what to do, which involves using your home folder "Get Info" window to convey the correct permissions. (Say it three times fast.)
As this article notes, use a Terminal command and a reboot to complete the process. For one of my migrated computers this worked beautifully! Forward and upward! For the other, but this solution did not help, and I faced a drunk Mac and the possibility of an unhappy user. So what I did (and what finally solved the problem) was the following:
- I dried the Mac and reinstalled Mojave using MacOS Recovery.
- I tried the move using another method; the first round, I had connected the two Maces together for Migration Assistant. Secondly, I used a Time Machine backup.
Now I'm not sure why just repeat the process solved the problem. Why was the transfer initially damaged? (I suspect that any Mac over five years hates me but I can not prove it.) But if this problem happens to you and Apple's permission solution does not fix it, I suggest you try it out above.  And finally it's a good time to point out the best methods for moving data to a new Mac. As Apple notes in a link I posted over, make sure both Macs are as updated as they can be. This means that you create a temporary user account on the new Mac to check for updates before continuing with Migration Assistant manually (instead of using Setup Assistant to transfer data immediately after you turn on your computer). If everything else is wrong, you may be exposed to moving your files manually, rather than migrating them, which is a big old pain, for sure. The last time I did, it took hours to get everything in place and worked properly, so if you can avoid it, do! Even if it means repeating a migration.
Do not drive yourself madly with concern about the problem like I did. I'm still recovering from it.